An enormous flying fox colony at Batemans Bay in south-east New South Wales has impacted house prices, according to a local property valuer.

Residents feared that the colony, which peaked at more than 100,000 fruit bats, was affecting the market.

"You wouldn't want to sell your home or your unit when they're here because there's no way in the world anybody would want to buy into this area," said Raelene, a resident living next to the colony at the Water Gardens.

"It's making a difference to the value of our properties."

Director of MVS Valuers at Batemans Bay, Blake McKenzie, looked into three property sales near the roosts since August 2015.

He said they sold for between $205,000 and $220,000, while the asking price for one of the properties was around $250,000.

"When looking at the adjoining properties in relation to other comparable properties that are unaffected [by the flying foxes] … the properties that adjoin the colony were generally $20,000 to $30,000 below market for comparable properties in similar localities," he said.

He said the market had taken the colony into consideration.

"Notwithstanding other forces in play with the property itself but [one] subject property was on the market for 1,700-plus days," Mr McKenzie said.

"So [the colony] does come into effect especially when people come and do an inspection, and while they're there they can see, hear and smell the colony next door."

But one Batemans Bay real estate agent said house prices had always been cheaper around the Water Gardens.

"Are the [flying foxes] having an impact on pricing going down in that area? I don't think so. I think people's memories are short. The bats will leave eventually," Robert McBride from Elders Real Estate in Batemans Bay said.

But he added people should hold off from selling right now.

"My advice would be not to sell at the moment and wait until things improve," he said.

"Some of the ones that have been on the market for such a long time, realistically they haven't sold because they're over-priced."

Blake McKenzie said properties around the Water Gardens may never reach the same level as the others unaffected by the colony due to other factors.

"But I do expect that once [the flying foxes] are gone, you may see an increase in values back in line with comparable properties," he said.

But Mr McKenzie added there was still a threat of the flying foxes returning, which meant there was a higher risk associated with properties next to the colonies.

The New South Wales Government has committed $2.5 million to solving the problem of flying foxes in Batemans Bay, describing the situation as a "state of emergency".